The high cost of fluorogenic probes used in quantitative PCR (qPCR) assays has prompted schemes that use “Universal Probes.” A Universal Probe, sometimes called a “Universal Template Probe,” is a generic fluorogenic probe that can be used to generate signal in qPCR assays by recognizing non-template specific sequences introduced into amplification products. One of the advantages of this method is that different target DNA sequences can be detected employing the same labeled probe, which substantially reduces the cost of real-time PCR set-up. One example, described by Zhang et al., 2003, Nucl. Acids Res. 31:e123, is a TaqMan™ probe that recognizes an approximately 20 base sequence from the 5′ end of a PCR primer. U.S. Pat. Nos. 7,153,658 and 7,601,821 describe variations of this scheme by adding a generic set of primers to the Universal Probe. In these approaches, a multiplex ligation reaction is performed to associate each specific target segment with its own pair of encoding PCR primers.